Pokemon: Tainted Souls
by LightlesShadow
Summary: After defeating Silver and being tasked with the completion of the Pokedex, Lyra decides to search for clues to find her missing father as she starts her journey. However, encounters with Team Rocket and Champion Lance complicates her originally intended goal as she is unintentionally wrapped in a much darker scheme of the Pokemon world that she have never known.


**Summary: Lyra, after defeating Silver and being tasked with completing the Pokedex, decides to search for clues to find her missing father as she starts her journey. However, encounters with Team Rocket and Champion Lance complicates her originally intended goal as she is unintentionally wrapped in a much larger and darker scheme of the Pokemon world that she never knew.**

 **KAEN = CYNDAQUIL**

 **CYNDAQUIL = KAEN**

 **Pokemon: Tainted Soul**

 **Chapter 1: So Unexpected**

I don't think I remember the last time I've seen Dad. All I remember was that I was eight when he left, leaving Mom to be a crying mess and vanishing into the darkness of night. I remember laying in bed, listening to the screams of both my parents. They seemed to be in some kind of verbal fight but I didn't know what they were yelling about.

I wanted to cover my ears and drown out their screams. However, no matter how much I covered my ears I always heard their yells through my hands. I closed my eyes tightly as tears streamed down my cheeks and soaked my comforter.

That was the first and last time my parents fought. Father was always a blurry image in the minimal memories that I've had of him. However, I've always associated him with positive feelings. He would always take us out to the caves, forest, and local daycare next door. He would always use his Pokemon, a Fearow, to follow me around whenever they weren't there to supervise.

On that day, I heard the front door to our house slam shut in the darkness of the night. I heard Mom weeping downstairs but I dared not move out of bed. I dared not make a single movement in hopes that this was all a dream. _Yeah,_ I thought at the time. This was all a dream. And it was with that false sense of security that I was lulled into slumber. Not knowing that my family would be broken the next day.

I heard the chirp of Pidgeys signal the start of a new day. I am eighteen now, the events of ten years ago have faded into a distant past but were still prevalent in my memories. I yawned and got out of bed. The weather was a blessing today. After cleaning up, I went downstairs.

Mom was sitting in one of the chairs at our dining table. She noticed my presence and walked up to me.

"Good morning, Lyra. Your friend Ethan was just here. He was playing hide and seek with his Marill. Oh, I almost forgot! Professor Elm was looking for you. He said he had a favor to ask of you. His lab is right next door in case you forget," she said.

Then, she paused for a moment before giving me my bag and my trainer card as an afterthought. After that, Mom went back to her seat and I headed out towards the door.

I wondered what Professor Elm wanted me to do. I had known the professor since the day the daycare in New Bark Town moved elsewhere. That daycare was owned by Ethan's grandparents and the space was perfect for Professor Elm to conduct his Pokemon evolution research. I was ten at the time so I easily adapted to the change of people in the small town.

As I closed the door behind me, Ethan's Marill came crashing into me. I stood shocked for a moment before Ethan left Professor Elm's lab and his Marill came running towards him. It jumped a few times before Ethan and his Marill walked away. I smiled at the sight. Ethan was always there for me whenever I needed it. He was one of my few friends that I felt comfortable around and was there to cheer me up when father vanished. An added bonus was that he was always kind to his Pokemon.

After Ethan left, I went to Professor Elm's lab. I greeted Ethan's father at the entrance, an assistant researcher to Professor Elm, and walked up to the professor. After acknowledging my presence, he gave a sunny smile and spoke promptly. "Hi, Lyra! You sure didn't sleep in this time. That's for sure," he laughed for a bit before he continued. "Anyway, do you know anything about my research? As you know, Pokemon are carried in Pokeballs these days, however, before they were invented, people use to walk with their Pokemon. Pokeballs are great in that you could carry a lot of Pokemon but there should be advantages to walking with your Pokemon. This must have to do with evolution so I'm going to give you a Pokemon!"

Surprise crossed my features as I didn't expect this from Professor Elm. When I was little, after the daycare center moved, I always came by Professor Elm's lab to play with the starters to the point that I was familiar with them. I knew each of them by heart, however, to be able to choose one was an entirely different matter.

He got an email before he could go any further and tell me what his favor was. He read the email with a focused eye. His eyes swept across the screen as he did so. After he was done, he turned towards me. "Hmm…okay. Hey, listen. I have this acquaintance that people call Mr. Pokemon. He keeps finding weird things and raving about his discoveries. Anyway, I just got his email saying that this time its for real. It's probably another Pokemon egg but we're still so busy with our research..." He drifted off for a moment before an expression of realization crossed his face. He hit his fist against his palm as if he came up with the most brilliant idea ever and pointed his finger at me. "Hey, why don't you go in our place? I know I could trust you with this task as long as you choose one of the Pokemon from the machine."

I looked at Professor Elm for a bit before walking in front of the machine. Once I was in front of it, the glass guarding the Pokeballs opened. I examined each and every one of them before settling on Cyndaquil, my favorite among the cute three starters.

After choosing Cyndaquil, it released itself from its Pokeball and appeared right next to me. She seemed to realize that I was there before she walked up towards me and rubbed her fur against my leg. She was pulsing with a warmth that I was familiar with. I bent down and patted her head. She gave a small and cute squeak in acknowledgment before jumping into my arms. Fortunately, the fire on her back was not activated or else I would have gotten burn marks on my arms.

"Do you want to nickname it?" asked Professor Elm.

I thought about it for a moment before turning to Cyndaquil. "How's Kaen?" I asked it. Cyndaquil, probably too elated that I chose it to be my partner, let out a squeak of acknowledgment before nestling herself against my arm.

Professor Elm chuckled at the sight before giving me further instructions. "Mr. Pokemon's house is past Cherrygrove City and you could walk your Pokemon to it. If your Pokemon ever get hurt, you could either use this machine behind me or go to a nearby Pokemon Center to heal it up. I'm counting on you, Lyra!"

As I walked out of the lab, Ethan's father stopped me and gave me some potions. He explained how Pokemon were weak at first and that it was best to have some Potions on for extra measure. I couldn't agree more, what he said was absolutely correct.

After leaving the lab, Ethan and his Marill were waiting for me outside. After noticing my presence, his Marill hopped up and down in excitement, circling Ethan before he even noticed that I was there.

"Lyra! So you picked a...Cyndaquil!" he exclaimed as he stared at the Pokemon in my arms with affection. "That Cyndaquil always liked you when you were little. You were always each other's favorites!"

"Yeah, I'm so happy that Kaen is my partner now, and my first ever," I said happily.

"Is that its nickname?" Ethan asked.

"Yeah, it's a Chinese word for flame that I thought would fit this little girl perfectly even when it evolves!" I exclaimed.

"That's great! Oh, yeah. Why don't you show it to your mom? I bet she would want to see such a cute Pokemon!" Ethan exclaimed before he went back to his house. As he walked, Marill paused and stared at Kaen for a few seconds before returning to Ethan's side. Kaen was next to me now as I had put her down while I spoke with Ethan.

I greeted Mom when I went home. She was sitting at the dining room table and contemplating something as she tapped her pen against the table. I tapped her on the shoulder before she could continue her thoughts.

"Oh, Lyra! Sorry, I was spacing off again," she explained and then noticed Kaen behind me. "Is that your Pokemon!? That's so cute!" She exclaimed as she bent down and petted Kaen on the head.

"Yeah, Professor Elm gave her to me. For my safety, he wanted me to take a Pokemon along in case I got attacked while going to Mr. Pokemon's house to retrieve a rare egg," I explained the details to her.

"That does sound a little difficult. However, when someone asks that kind of favor of you. That means that they trust you," she said happily with a smile on her face. Then, almost as an afterthought, she took out a familiar device from her pocket and handed it to me. It seemed to be some kind of watch with a touchable screen. "Oh, yeah! You're Pokegear came back from the repair shop. Here you go!"

I affixed the PokeGear to my wrist and turned it on. All the functions were working properly and I gave Mom a thumbs up to show her that it was okay. She gave me the same smile before going into the kitchen to fix up some food. I left the house and was about to head out into the wild grass before Professor Elm stopped me.

"Wait one second!" he shouted. I turned around at the sound of his voice as he ran up to me. He heaved a few breaths before bringing up his wrist with his PokeGear in front of me. "Let's register each other's number."

I agreed and we both registered each other's numbers.

"I'll call you if anything happens," he said.

I nodded my head and decided to head out then. As I made my way through the great unknown, accompanied by Kaen, I gulped as I made my way through the wild grass. I attempted to walk as covertly as possible but to no avail. A wild Pidgey flew out of nowhere and glared Kaen down.

"Go, Kaen!" I commanded.

Kaen prepared for battle and glared at Pidgey. The Pidgey lunged at Kaen and Kaen did the same. Pidgey stumbled back and swiped sand off the ground.

"Kaen, dodge it and use Tackle again!" I commanded. Kaen gave a slight sound of obedience before she dodged the Sand Attack and tackled the Pidgey once more, making it faint this time. The Pidgey disappeared into the grass and as we walked through the wild grass, another wild Pokemon appeared. Kaen defeated the Sentret but it never moved from its position so I had to cautiously pick it up and move it to the side.

After that, we made it to Cherrygrove City without incident. Kaen and I looked at each other before letting our a small laugh; this was our first trip together and we were both very nervous. It wasn't long before our moment together was interrupted by the voice of an old man calling out to us.

"Hey, kiddo! Did you just come here from NewBark town? You must be a rookie trainer then! If that's the case then I can teach you a few things," he said giddily.

I was about to refuse his offer but he took me my the wrist and ran towards the nearest building, a Pokemon Center. _This elderly man could run!?_ I thought in disbelief as I attempted to keep up with him but my shoes apparently weren't made for running.

I stumbled and Kaen panicked as she saw me about to fall over. She made a sound of warning before gathering herself and coming in front of me to break my fall. But before I could crush her, I found my balance and let out a sigh of relief.

"I apologize for that. I didn't know that you weren't wearing running shoes," explained the man as he bowed in apology.

"It's quite alright," I hurried to quell any of his worries. "Anyway, weren't you going to do a tour? I would like to learn more about the main functions that a beginning trainer like me would need to know."

The man appeared shocked for a moment before he wiped the tears that threatened to fall and continued on his tour of what a Pokemon trainer needed to know. He explained how the Pokemon Center and Pokestore worked. He then showed us the beach and then brought us to the entrance of his house.

He bowed to me as the tour concluded. "Kiddo, as thanks for letting me pretend to be a tour guide and for almost making you fall over, I would like you to have these running shoes."

I smiled and thanked him but looked at the shoes. He laughed when he saw the skeptical look on my face.

"Kiddo, those shoes are brand new. This is the first time I ever wore them!" exclaimed the old man as he laughed once again and sauntered into his own house. I watched as the door closed behind him and looked at Kaen. She also gave me the same dubious look and we both shrugged our shoulders at the same time.

With the running shoes, I kept on competing with Kaen on who would be faster. However, at the same time, we battled more wild Pokemon frequently in which Kaen kept on gaining more experience points to the point that by the time we reached Mr. Pokemon's house, she elevated to Level 9.

I knocked on the house that I assumed belonged to Mr. Pokemon but the middle-aged man who opened the door sighed as he looked at me. "If you think that I am Mr. Pokemon you are mistaken."

I was taken aback for a moment, wondering how he read my thoughts before I asked. "Then...who are you then?"

"I'm someone who tinkers around with Apricorns and experiment with them," introduced the man. "Here, as a gift for getting this far on your journey, I would give you this," He said as he handed over what seemed to be a case that specialized in hold apricorns.

"Thank you!" I bowed my head in appreciation and made my way out of his house. It was better that I finished Professor Elm's task before I got carried away. I, at least, knew the basic functions of Apricorns. The more apricorns one collects the more unique Pokeballs that one could acquire by getting them made by a man named Mr. Kurt. I've heard of him to be a master in creating different Pokeballs but that was about all. But it was still interesting to see how something natural like an apricorn could turn into something mechanical like a Pokeball. The mysteries of the universe sure was mystical.

As I headed deeper into Route 30, I noticed some Pokemon trainers battling and took a detour to get to Mr. Pokemon's real house this time. I knocked on the door again, hoping that it would be Mr. Pokemon. An old man opened the door and gave me a skeptical look before an expression of realization crossed his features.

"Oh! You must be the assistant that Professor Elm was speaking of!" he exclaimed. "Excellent! Excellent! I would get the Egg here in a moment," he said as he went to the back of his room and shuffled around through his cases before producing an egg. He came back cautiously holding a peculiar colored egg in his hands. He handed it to me with such gentleness that I knew that if I dropped this egg, I would never hear the end of it from Professor Elm.

As I securely had a hold on the Egg, another elderly man dressed in a lab coat walked up to me. He looked at Kaen who was standing next to my leg and then at me. Then, he smiled and held out his hand.

"My name is Professor Oak, a Pokemon researcher. I'm here to visit Mr. Pokemon, an old friend of mine. So...you are Lyra. That's quite the rare Pokemon that you have there. I take it that you are helping with Elm's research?" he inquired.

I nodded my head.

"You seem to be quite the dependable trainer, Lyra. That Cyndaquil of yours is already attached to you even though you haven't had it for long," Oak observed.

"Well, I knew this little guy since I was young. I used to go to Professor Elm's lab and play with the starters all the time," I explained to Oak.

"Usually, Pokemon would be very weary of people no matter how much time you spend with them. However, you seem different, you have a natural skill for befriending Pokemon and unlocking their true potential," he complimented. "With that, I would like to give you the latest version of the Pokedex. I hope you would find that machine useful and also help me in completing that Pokedex."

 _Wait...I'm already getting an important device right off the bat despite not even being on a legit journey yet?_ I thought. The implication of carrying the Pokedex opening a wide array of possibilities in my head.

"Now, I should take my leave now. I have stayed here long enough," Professor Oak said as he sauntered towards the door and left. I stared at the spot where he left before looking at the Pokedex in my hand. I couldn't believe that I was given the task of completing the Pokedex without any prior notice. Regardless, this was more of a benefit than a hazard and I was going to make the best of it.

As Mr. Pokemon kindly healed up Kaen and said farewell, I got an abrupt phone call from Professor Elm.

When I answered his call, he seemed to be in a panic.

"H-Hello? Lyra?" asked Professor Elm in a shaky voice.

Something felt terribly wrong. "What's wrong Professor Elm?"

"This is bad! This is so bad! One of the Pokemon at the lab just got stolen and I don't know who did it!" he cried hysterically through the PokeGear. "P-Please come back as soon as possible. We need your help with this!"

My eyes widened at this startling new development. It was rare to hear of any crimes happening in New Bark Town, that was one of the reasons why my family have been living there for quite some time because it was considered to be one of the more safer places in Johto. But this...I didn't know about this.

 _A Pokemon at the lab got stolen!_ _How!?_

 **A/N: This story closely follows the events of HeartGold and SoulSilver but with wide divergences. Though the plot is roughly the same as the original, I would be adding more depth and layer to the characters and reveal a darker side of Lance that the fanbase may not be used to. Hence, the darker title for the series.**


End file.
